Biology has contradictory relationships with randomness. First, it is a complex issue for an empirical science to ensure that apparently random events are truly random, this being further complicated by the loose definitions of unpredictability used in the discipline. Second, biology is made up of many different fields, which have different traditions and procedures for considering random events. Randomness is in many ways an inherent feature of evolutionary biology and genetics. Indeed, chance/Darwinian selection principles, as well as the combinatorial genetic lottery leading to gametes and fertilisation, rely, at least partially, on probabilistic laws that refer to random events. On the other hand, molecular biology has long been based on deterministic premises that have led to a focus on the precision of molecular interactions to explain phenotypes, and, consequently, to the relegation of randomness to the marginal status of ‘noise’. However, recent experimental results, as well as new theoretical frameworks, have challenged this view and may provide unifying explanations by acknowledging the intrinsic stochastic dimension of intracellular pathways as a biological parameter, rather than just as background noise. This should lead to a significant reappraisal of the status of randomness in the life sciences, and have important consequences on research strategies for theoretical and applied biology.

A process $M$ terminates if it cannot produce an infinite sequence of reductions $M \mathop{\rightarrow}^{\tau} M_1\mathop{\rightarrow}^{\tau} M_2 \ldots$. Termination is a useful property in concurrency. For instance, a terminating applet, when loaded on a machine, will not run for ever, possibly absorbing all computing resources (a ‘denial of service’ attack). Similarly, termination guarantees that queries to a given service originate only finite computations.

We ensure termination of a non-trivial subset of the $\pi$-calculus by a combination of conditions on types and on the syntax. The proof of termination is in two parts. The first uses the technique of logical relations – a well-know technique of $\lambda$-calculi – on a small set of non-deterministic ‘functional’ processes. The second part of the proof uses techniques of process calculi, in particular, techniques of behavioural preorders.

We define a strongly normalising proof-net calculus corresponding to the logic of strongly compact closed categories with biproducts. The calculus is a full and faithful representation of the free strongly compact closed category with biproducts on a given category with an involution. This syntax can be used to represent and reason about quantum processes.

We consider types and typed lambda calculus over a finite number of ground types. We are going to investigate the size of the fraction of inhabited types of the given length n against the number of all types of length n. The plan of this paper is to find the limit of that fraction when n → ∞. The answer to this question is equivalent to finding the ‘density’ of inhabited types in the set of all types, or the so-called asymptotic probability of finding an inhabited type in the set of all types. Under the Curry–Howard isomorphism this means finding the density or asymptotic probability of provable intuitionistic propositional formulas in the set of all formulas. For types with one ground type (formulas with one propositional variable), we prove that the limit exists and is equal to 1/2 + √5/10, which is approximately 72.36%. This means that a long random type (formula) has this probability of being inhabited (tautology). We also prove that for every finite number k of ground-type variables, the density of inhabited types is always positive and lies between (4k + 1)/(2k + 1)2 and (3k + 1)/(k + 1)2. Therefore we can easily see that the density is decreasing to 0 with k going to infinity. From the lower and upper bounds presented we can deduce that at least 1/3 of classical tautologies are intuitionistic.

Tissue P systems are a class of bio-inspired computing models motivated by biochemical interactions between cells in a tissue-like arrangement. Tissue P systems with cell division offer a theoretical device to generate an exponentially growing structure in order to solve computationally hard problems efficiently with the assumption that there exists a global clock to mark the time for the system, the execution of each rule is completed in exactly one time unit. Actually, the execution time of different biochemical reactions in cells depends on many uncertain factors. In this work, with this biological inspiration, we remove the restriction on the execution time of each rule, and the computational efficiency of tissue P systems with cell division is investigated. Specifically, we solve subset sum problem by tissue P systems with cell division in a time-free manner in the sense that the correctness of the solution to the problem does not depend on the execution time of the involved rules.

Ptolemy‡ is an open-source and extensible modelling and simulation framework. It offers heterogeneous modeling capabilities by allowing different models of computation, both untimed and timed, to be composed hierarchically in an arbitrary fashion. This paper proposes a formal semantics for Ptolemy that is modular in the sense that atomic actors and their compositions are treated in a unified way. In particular, all actors conform to an executable interface that contains four functions: fire (produce outputs given current state and inputs); postfire (update state instantaneously); deadline (how much time the actor is willing to let elapse); and time-update (update the state with the passage of time). Composite actors are obtained using composition operators that in Ptolemy are called directors. Different directors realise different models of computation. In this paper, we formally define the directors for the following models of computation: synchronous- reactive, discrete event, continuous time, process networks and modal models.

The notion of tripos (Hyland et al. 1980; Pitts 1981) was motivated by the desire to explain in what sense Higg's description of sheaf toposes as H-valued sets and Hyland's realizability toposes are instances of the same construction. The construction itself can be seen as the universal solution to the problem of realizing the predicates of a first order hyperdoctrine as subobjects in a logos with effective equivalence relations. In this note it is shown that the resulting logos is actually a topos if and only if the original hyperdoctrine satisfies a certain comprehension property. Triposes satisfy this property, but there are examples of non-triposes satisfying this form of comprehension.

We develop category theory within Univalent Foundations, which is a foundational system for mathematics based on a homotopical interpretation of dependent type theory. In this system, we propose a definition of ‘category’ for which equality and equivalence of categories agree. Such categories satisfy a version of the univalence axiom, saying that the type of isomorphisms between any two objects is equivalent to the identity type between these objects; we call them ‘saturated’ or ‘univalent’ categories. Moreover, we show that any category is weakly equivalent to a univalent one in a universal way. In homotopical and higher-categorical semantics, this construction corresponds to a truncated version of the Rezk completion for Segal spaces, and also to the stack completion of a prestack.

We present a higher-order call-by-need lambda calculus enriched with constructors, case expressions, recursive letrec expressions, a seq operator for sequential evaluation and a non-deterministic operator amb that is locally bottom-avoiding. We use a small-step operational semantics in the form of a single-step rewriting system that defines a (non-deterministic) normal-order reduction. This strategy can be made fair by adding resources for book-keeping. As equational theory, we use contextual equivalence (that is, terms are equal if, when plugged into any program context, their termination behaviour is the same), in which we use a combination of may- and must-convergence, which is appropriate for non-deterministic computations. We show that we can drop the fairness condition for equational reasoning, since the valid equations with respect to normal-order reduction are the same as for fair normal-order reduction. We develop a number of proof tools for proving correctness of program transformations. In particular, we prove a context lemma for both may- and must- convergence that restricts the number of contexts that need to be examined for proving contextual equivalence. Combining this with so-called complete sets of commuting and forking diagrams, we show that all the deterministic reduction rules and some additional transformations preserve contextual equivalence. We also prove a standardisation theorem for fair normal-order reduction. The structure of the ordering ≤c is also analysed, and we show that Ω is not a least element and ≤c already implies contextual equivalence with respect to may-convergence.

This paper unveils and motivates an ambitious programme of hidden algebraic research in software engineering. We begin with an outline of our general goals, continue with an overview of results, and conclude with a discussion of some future plans. The main contribution is powerful hidden coinduction techniques for proving behavioural correctness of concurrent systems, and several mechanical proofs are given using OBJ3. We also show how modularization, bisimulation, transition systems, concurrency and combinations of the functional, constraint, logic and object paradigms fit into hidden algebra.

This paper presents general syntactic conditions ensuring the strong normalisation and the logical consistency of the Calculus of Algebraic Constructions, an extension of the Calculus of Constructions with functions and predicates defined by higher-order rewrite rules. On the one hand, the Calculus of Constructions is a powerful type system in which one can formalise the propositions and natural deduction proofs of higher-order logic. On the other hand, rewriting is a simple and powerful computation paradigm. The combination of the two allows, among other things, the development of formal proofs with a reduced size and more automation compared with more traditional proof assistants. The main novelty is to consider a general form of rewriting at the predicate-level that generalises the strong elimination of the Calculus of Inductive Constructions.

This paper axiomatises the structure of bigraphs, and proves that the resulting theory is complete. Bigraphs are graphs with double structure, representing locality and connectivity. They have been shown to represent dynamic theories for the $\pi$-calculus, mobile ambients and Petri nets in a way that is faithful to each of those models of discrete behaviour. While the main purpose of bigraphs is to understand mobile systems, a prerequisite for this understanding is a well-behaved theory of the structure of states in such systems. The algebra of bigraph structure is surprisingly simple, as this paper demonstrates; this is because bigraphs treat locality and connectivity orthogonally.

We describe a non-extensional variant of Martin-Löf type theory, which we call two-dimensional type theory, and equip it with a sound and complete semantics valued in 2-categories.

We propose a semantic framework for dynamic systems, which, in a sense, extends the well-known algebraic approach for modelling static data structures to the dynamic case. The framework is based on a new mathematical structure, called a d-oid, consisting of a set of instant structures and a set of dynamic operations. An instant structure is a static structure, e.g. an algebra; a dynamic operation is a transformation of instant structures with an associated point to point map, which allows us to keep track of the transformations of single objects and thus is called a tracking map. By an appropriate notion of morphism, the d-oids over a dynamic signature constitute a category.

It is shown that d-oids can model object systems and support an abstract notion of possibly unique object identity; moreover, for a d-oid satisfying an identity preserving condition, there exists an essentially equivalent d-oid where the elements of instant structures are just names.

We develop temporal logic from the theory of complete lattices, Galois connections and fixed points. In particular, we prove that all seventeen axioms of Manna and Pnueli's sound and complete proof system for linear temporal logic can be derived from just two postulates, namely that ([oplus ], &[ominus ]tilde;) is a Galois connection and that ([ominus ], [oplus ]) is a perfect Galois connection. We also obtain a similar result for the branching time logic CTL.

A surprising insight is that most of the theory can be developed without the use of negation. In effect, we are studying intuitionistic temporal logic. Several examples of such structures occurring in computer science are given. Finally, we show temporal algebra at work in the derivation of a simple graph-theoretic algorithm.

This paper is tutorial in style and there are no difficult technical results. To the experts in temporal logics, we hope to convey the simplicity and beauty of algebraic reasoning as opposed to the machine-orientedness of logical deduction. To those familiar with the calculational approach to programming, we want to show that their methods extend easily and smoothly to temporal reasoning. For anybody else, this text may serve as a gentle introduction to both areas.

Every finitary endofunctor of $\Set$ is proved to generate a free iterative theory in the sense of Elgot. This work is based on coalgebras, specifically on parametric corecursion, and the proof is presented for categories more general than just $\Set$.

We propose a graphical implementation for (possibly recursive) processes of the π-calculus, encoding each process into a graph. Our implementation is sound and complete with respect to the structural congruence for the calculus: two processes are equivalent if and only if they are mapped into graphs with the same normal form. Most importantly, the encoding allows the use of standard graph rewriting mechanisms for modelling the reduction semantics of the calculus.

Differential linear logic enriches linear logic with additional logical rules for the exponential connectives, dual to the usual rules of dereliction, weakening and contraction. We present a proof-net syntax for differential linear logic and a categorical axiomatization of its denotational models. We also introduce a simple categorical condition on these models under which a general antiderivative operation becomes available. Last, we briefly describe the model of sets and relations and give a more detailed account of the model of finiteness spaces and linear and continuous functions.

We show that the category whose objects are families of Markov processes on Polish spaces, with a given transition kernel, and whose morphisms are transition probability preserving, surjective continuous maps has semi-pullbacks, i.e., for any pair of morphisms fi:Si→S (i = 1, 2), there exists an object V and morphisms πi:V→Si (i = 1, 2) such that f1∘π1 = f2∘π2. This property holds for various full subcategories, including that of families of Markov processes on locally compact second countable spaces, and in the larger category where the objects are families of Markov processes on analytic spaces and morphisms are transition probability preserving surjective Borel maps. It also follows that the category of probability measures on Polish spaces and measure-preserving continuous surjective maps has semi-pullbacks. A main consequence of our result is that probabilistic bisimulation for labelled Markov processes on all these categories, defined in terms of spans of morphisms, is an equivalence relation.

We show that the model of quantum computation based on density matrices and superoperators can be decomposed into a pure classical (functional) part and an effectful part modelling probabilities and measurement. The effectful part can be modelled using a generalisation of monads called arrows. We express the resulting executable model of quantum computing in the Haskell programming language using its special syntax for arrow computations. However, the embedding in Haskell is not perfect: a faithful model of quantum computing requires type capabilities that are not directly expressible in Haskell.